Starting phenix.real_space_refine on Wed Mar 12 20:47:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z2g_14465/03_2025/7z2g_14465.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2g_14465/03_2025/7z2g_14465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z2g_14465/03_2025/7z2g_14465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2g_14465/03_2025/7z2g_14465.map" model { file = "/net/cci-nas-00/data/ceres_data/7z2g_14465/03_2025/7z2g_14465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2g_14465/03_2025/7z2g_14465.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 35 5.49 5 S 14 5.16 5 Cl 1 4.86 5 C 5323 2.51 5 N 1401 2.21 5 O 1629 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8406 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4324 Classifications: {'peptide': 536} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 499} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3333 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 30, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 720 Classifications: {'DNA': 34, 'RNA': 2} Modifications used: {'5*END': 1, 'rna3p': 2} Link IDs: {'rna3p': 35} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan2': 1, ' DA%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'2KW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.41, per 1000 atoms: 0.64 Number of scatterers: 8406 At special positions: 0 Unit cell: (98.94, 109.61, 97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 14 16.00 P 35 15.00 F 3 9.00 O 1629 8.00 N 1401 7.00 C 5323 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 893.6 milliseconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 12 sheets defined 40.5% alpha, 15.4% beta 13 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 removed outlier: 3.581A pdb=" N GLU A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 114 through 118 removed outlier: 4.096A pdb=" N VAL A 118 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 4.593A pdb=" N LYS A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.666A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.872A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 311 Processing helix chain 'A' and resid 363 through 383 Processing helix chain 'A' and resid 394 through 404 removed outlier: 3.656A pdb=" N GLU A 404 " --> pdb=" O THR A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 489 Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.563A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.530A pdb=" N ASN A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 4.537A pdb=" N GLN A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 552 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 removed outlier: 3.695A pdb=" N GLU B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 removed outlier: 3.932A pdb=" N ASP B 67 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 removed outlier: 3.765A pdb=" N LYS B 82 " --> pdb=" O ARG B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.794A pdb=" N LYS B 101 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.925A pdb=" N LYS B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 154 through 175 removed outlier: 3.976A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.698A pdb=" N ARG B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 253 through 269 removed outlier: 4.142A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.716A pdb=" N GLU B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 363 removed outlier: 4.470A pdb=" N ALA B 360 " --> pdb=" O ARG B 356 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS B 361 " --> pdb=" O MET B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.835A pdb=" N TRP B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.673A pdb=" N GLN A 145 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 143 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 331 removed outlier: 3.898A pdb=" N GLU A 328 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 340 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR A 339 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR A 351 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN A 343 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LYS A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.938A pdb=" N THR A 362 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 512 " --> pdb=" O THR A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 391 removed outlier: 6.830A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 464 through 470 removed outlier: 4.373A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL A 493 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ALA A 534 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE A 495 " --> pdb=" O ALA A 534 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AA9, first strand: chain 'B' and resid 60 through 63 Processing sheet with id=AB1, first strand: chain 'B' and resid 105 through 110 removed outlier: 3.554A pdb=" N SER B 105 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 347 through 351 removed outlier: 8.574A pdb=" N ASN B 348 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLN B 343 " --> pdb=" O ASN B 348 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 347 through 351 removed outlier: 8.574A pdb=" N ASN B 348 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLN B 343 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 298 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1316 1.27 - 1.40: 2137 1.40 - 1.54: 5024 1.54 - 1.67: 193 1.67 - 1.81: 26 Bond restraints: 8696 Sorted by residual: bond pdb=" C10 2KW A 601 " pdb=" C9 2KW A 601 " ideal model delta sigma weight residual 1.354 1.522 -0.168 2.00e-02 2.50e+03 7.04e+01 bond pdb=" C21 2KW A 601 " pdb=" N20 2KW A 601 " ideal model delta sigma weight residual 1.356 1.499 -0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" C10 2KW A 601 " pdb=" N11 2KW A 601 " ideal model delta sigma weight residual 1.355 1.489 -0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" C7 2KW A 601 " pdb=" C8 2KW A 601 " ideal model delta sigma weight residual 1.359 1.481 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C18 2KW A 601 " pdb=" N19 2KW A 601 " ideal model delta sigma weight residual 1.287 1.402 -0.115 2.00e-02 2.50e+03 3.28e+01 ... (remaining 8691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 11854 3.06 - 6.11: 109 6.11 - 9.17: 10 9.17 - 12.23: 1 12.23 - 15.28: 1 Bond angle restraints: 11975 Sorted by residual: angle pdb=" C ASP A 186 " pdb=" CA ASP A 186 " pdb=" CB ASP A 186 " ideal model delta sigma weight residual 109.38 94.10 15.28 2.03e+00 2.43e-01 5.67e+01 angle pdb=" C CYS A 63 " pdb=" CA CYS A 63 " pdb=" CB CYS A 63 " ideal model delta sigma weight residual 109.66 120.31 -10.65 1.94e+00 2.66e-01 3.01e+01 angle pdb=" N ASP A 186 " pdb=" CA ASP A 186 " pdb=" C ASP A 186 " ideal model delta sigma weight residual 109.06 117.88 -8.82 1.70e+00 3.46e-01 2.69e+01 angle pdb=" N GLY B 155 " pdb=" CA GLY B 155 " pdb=" C GLY B 155 " ideal model delta sigma weight residual 113.86 107.18 6.68 1.50e+00 4.44e-01 1.98e+01 angle pdb=" C5' DG E 33 " pdb=" C4' DG E 33 " pdb=" O4' DG E 33 " ideal model delta sigma weight residual 109.40 115.87 -6.47 1.50e+00 4.44e-01 1.86e+01 ... (remaining 11970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 4321 17.27 - 34.55: 560 34.55 - 51.82: 159 51.82 - 69.09: 45 69.09 - 86.37: 10 Dihedral angle restraints: 5095 sinusoidal: 2344 harmonic: 2751 Sorted by residual: dihedral pdb=" C ASP A 186 " pdb=" N ASP A 186 " pdb=" CA ASP A 186 " pdb=" CB ASP A 186 " ideal model delta harmonic sigma weight residual -122.60 -107.57 -15.03 0 2.50e+00 1.60e-01 3.61e+01 dihedral pdb=" CA ILE A 411 " pdb=" C ILE A 411 " pdb=" N PRO A 412 " pdb=" CA PRO A 412 " ideal model delta harmonic sigma weight residual -180.00 -160.56 -19.44 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PHE A 77 " pdb=" C PHE A 77 " pdb=" N ARG A 78 " pdb=" CA ARG A 78 " ideal model delta harmonic sigma weight residual -180.00 -161.62 -18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1181 0.083 - 0.166: 115 0.166 - 0.249: 7 0.249 - 0.332: 1 0.332 - 0.415: 2 Chirality restraints: 1306 Sorted by residual: chirality pdb=" C4' DG E 32 " pdb=" C5' DG E 32 " pdb=" O4' DG E 32 " pdb=" C3' DG E 32 " both_signs ideal model delta sigma weight residual False -2.53 -2.11 -0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" C4' DG E 33 " pdb=" C5' DG E 33 " pdb=" O4' DG E 33 " pdb=" C3' DG E 33 " both_signs ideal model delta sigma weight residual False -2.53 -2.15 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" C4' DC E 22 " pdb=" C5' DC E 22 " pdb=" O4' DC E 22 " pdb=" C3' DC E 22 " both_signs ideal model delta sigma weight residual False -2.53 -2.26 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1303 not shown) Planarity restraints: 1388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 358 " 0.492 9.50e-02 1.11e+02 2.20e-01 2.97e+01 pdb=" NE ARG A 358 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 358 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 358 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 358 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 467 " -0.087 5.00e-02 4.00e+02 1.30e-01 2.70e+01 pdb=" N PRO A 468 " 0.225 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 414 " 0.014 2.00e-02 2.50e+03 1.92e-02 9.19e+00 pdb=" CG TRP B 414 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 414 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP B 414 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 414 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 414 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 414 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 414 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 414 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 414 " 0.001 2.00e-02 2.50e+03 ... (remaining 1385 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2631 2.84 - 3.35: 7457 3.35 - 3.87: 13733 3.87 - 4.38: 15986 4.38 - 4.90: 26814 Nonbonded interactions: 66621 Sorted by model distance: nonbonded pdb=" O VAL A 35 " pdb=" OG1 THR A 39 " model vdw 2.324 3.040 nonbonded pdb=" OH TYR B 115 " pdb=" OE1 GLN B 182 " model vdw 2.360 3.040 nonbonded pdb=" OG1 THR A 107 " pdb=" NE2 HIS A 198 " model vdw 2.371 3.120 nonbonded pdb=" O LYS B 366 " pdb=" OE1 GLU B 370 " model vdw 2.382 3.040 nonbonded pdb=" O LYS A 103 " pdb=" N20 2KW A 601 " model vdw 2.383 3.120 ... (remaining 66616 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.270 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.168 8696 Z= 0.339 Angle : 0.743 15.282 11975 Z= 0.412 Chirality : 0.049 0.415 1306 Planarity : 0.008 0.220 1388 Dihedral : 16.930 86.367 3319 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.24 % Allowed : 1.57 % Favored : 98.19 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.27), residues: 931 helix: 0.63 (0.31), residues: 316 sheet: -0.91 (0.40), residues: 151 loop : -0.91 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP B 414 HIS 0.003 0.001 HIS A 315 PHE 0.011 0.001 PHE B 130 TYR 0.027 0.001 TYR A 405 ARG 0.003 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.814 Fit side-chains REVERT: A 164 MET cc_start: 0.8586 (tpp) cc_final: 0.7881 (tpp) REVERT: A 500 GLN cc_start: 0.7479 (mp10) cc_final: 0.7121 (mm-40) outliers start: 2 outliers final: 0 residues processed: 115 average time/residue: 0.1753 time to fit residues: 29.1518 Evaluate side-chains 83 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 75 optimal weight: 50.0000 chunk 29 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN B 255 ASN B 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.190109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.162939 restraints weight = 9103.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.160787 restraints weight = 12359.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.158864 restraints weight = 12161.210| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8696 Z= 0.240 Angle : 0.589 8.557 11975 Z= 0.305 Chirality : 0.043 0.167 1306 Planarity : 0.005 0.093 1388 Dihedral : 15.667 77.900 1369 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.08 % Allowed : 10.24 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.28), residues: 931 helix: 0.91 (0.30), residues: 322 sheet: -0.96 (0.39), residues: 156 loop : -0.88 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 383 HIS 0.004 0.001 HIS A 315 PHE 0.015 0.001 PHE B 61 TYR 0.011 0.001 TYR A 405 ARG 0.002 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 500 GLN cc_start: 0.7420 (mp10) cc_final: 0.7146 (mt0) REVERT: B 260 LEU cc_start: 0.8779 (tt) cc_final: 0.8556 (tp) outliers start: 9 outliers final: 7 residues processed: 99 average time/residue: 0.1880 time to fit residues: 26.8966 Evaluate side-chains 91 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 85 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 75 optimal weight: 50.0000 chunk 42 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.187165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.156575 restraints weight = 9327.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.153974 restraints weight = 15109.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.153921 restraints weight = 14883.463| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8696 Z= 0.306 Angle : 0.617 7.662 11975 Z= 0.317 Chirality : 0.044 0.169 1306 Planarity : 0.005 0.082 1388 Dihedral : 15.788 78.610 1369 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.05 % Allowed : 13.13 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.27), residues: 931 helix: 0.82 (0.30), residues: 330 sheet: -0.85 (0.40), residues: 149 loop : -1.00 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 153 HIS 0.005 0.001 HIS A 315 PHE 0.017 0.002 PHE B 130 TYR 0.011 0.002 TYR A 405 ARG 0.004 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: A 500 GLN cc_start: 0.7626 (mp10) cc_final: 0.7227 (mt0) outliers start: 17 outliers final: 13 residues processed: 98 average time/residue: 0.1845 time to fit residues: 26.8071 Evaluate side-chains 97 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 78 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 13 optimal weight: 0.0770 chunk 26 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 75 optimal weight: 40.0000 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 overall best weight: 3.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.188706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.158641 restraints weight = 9167.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.156374 restraints weight = 12856.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.156585 restraints weight = 13564.960| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8696 Z= 0.239 Angle : 0.566 6.258 11975 Z= 0.292 Chirality : 0.042 0.152 1306 Planarity : 0.004 0.073 1388 Dihedral : 15.743 77.927 1369 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.05 % Allowed : 14.46 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.27), residues: 931 helix: 0.96 (0.30), residues: 330 sheet: -0.78 (0.40), residues: 149 loop : -0.97 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 153 HIS 0.004 0.001 HIS A 315 PHE 0.013 0.001 PHE B 130 TYR 0.017 0.001 TYR B 319 ARG 0.004 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.875 Fit side-chains REVERT: A 500 GLN cc_start: 0.7614 (mp10) cc_final: 0.7199 (mt0) outliers start: 17 outliers final: 14 residues processed: 98 average time/residue: 0.1716 time to fit residues: 25.1991 Evaluate side-chains 94 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 63 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN B 182 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.187236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.156519 restraints weight = 9194.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.153760 restraints weight = 15699.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.155018 restraints weight = 15249.549| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8696 Z= 0.294 Angle : 0.600 9.841 11975 Z= 0.307 Chirality : 0.043 0.145 1306 Planarity : 0.004 0.051 1388 Dihedral : 15.864 77.388 1369 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.53 % Allowed : 15.54 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.27), residues: 931 helix: 0.89 (0.29), residues: 330 sheet: -0.90 (0.40), residues: 149 loop : -1.10 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 383 HIS 0.004 0.001 HIS A 315 PHE 0.028 0.002 PHE B 87 TYR 0.012 0.002 TYR B 319 ARG 0.003 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.813 Fit side-chains REVERT: A 500 GLN cc_start: 0.7592 (mp10) cc_final: 0.7208 (mt0) REVERT: B 346 PHE cc_start: 0.6178 (m-80) cc_final: 0.5624 (m-80) outliers start: 21 outliers final: 20 residues processed: 97 average time/residue: 0.1760 time to fit residues: 25.4661 Evaluate side-chains 97 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 28 optimal weight: 30.0000 chunk 40 optimal weight: 0.2980 chunk 31 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.188528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.158774 restraints weight = 9161.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.156059 restraints weight = 12775.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.155572 restraints weight = 13520.739| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8696 Z= 0.249 Angle : 0.569 9.055 11975 Z= 0.292 Chirality : 0.042 0.142 1306 Planarity : 0.004 0.052 1388 Dihedral : 15.854 76.606 1369 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.01 % Allowed : 16.14 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.27), residues: 931 helix: 0.99 (0.30), residues: 330 sheet: -0.93 (0.39), residues: 149 loop : -1.04 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 153 HIS 0.004 0.001 HIS A 315 PHE 0.017 0.001 PHE B 87 TYR 0.017 0.001 TYR B 319 ARG 0.004 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.822 Fit side-chains REVERT: A 500 GLN cc_start: 0.7603 (mp10) cc_final: 0.7194 (mt0) REVERT: B 346 PHE cc_start: 0.6084 (m-80) cc_final: 0.5547 (m-80) outliers start: 25 outliers final: 21 residues processed: 95 average time/residue: 0.1810 time to fit residues: 25.3128 Evaluate side-chains 99 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 71 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 81 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.187636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.157114 restraints weight = 9220.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.154819 restraints weight = 15196.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.155501 restraints weight = 16066.852| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8696 Z= 0.285 Angle : 0.601 9.059 11975 Z= 0.308 Chirality : 0.044 0.281 1306 Planarity : 0.004 0.058 1388 Dihedral : 15.937 76.136 1369 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.01 % Allowed : 16.75 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.27), residues: 931 helix: 0.93 (0.29), residues: 330 sheet: -1.03 (0.39), residues: 149 loop : -1.07 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 383 HIS 0.004 0.001 HIS A 315 PHE 0.016 0.001 PHE B 130 TYR 0.014 0.002 TYR B 319 ARG 0.004 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: A 500 GLN cc_start: 0.7578 (mp10) cc_final: 0.7209 (mt0) REVERT: B 346 PHE cc_start: 0.6164 (m-80) cc_final: 0.5669 (m-80) outliers start: 25 outliers final: 23 residues processed: 98 average time/residue: 0.1592 time to fit residues: 23.3451 Evaluate side-chains 99 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 HIS ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.189534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.159632 restraints weight = 9273.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.157761 restraints weight = 13702.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.158399 restraints weight = 13995.030| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8696 Z= 0.222 Angle : 0.562 8.097 11975 Z= 0.288 Chirality : 0.043 0.268 1306 Planarity : 0.004 0.059 1388 Dihedral : 15.816 75.046 1369 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.89 % Allowed : 17.47 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.27), residues: 931 helix: 1.06 (0.29), residues: 332 sheet: -0.99 (0.39), residues: 149 loop : -1.00 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 383 HIS 0.003 0.001 HIS A 315 PHE 0.012 0.001 PHE B 130 TYR 0.010 0.001 TYR B 319 ARG 0.003 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 500 GLN cc_start: 0.7566 (mp10) cc_final: 0.7203 (mt0) REVERT: B 346 PHE cc_start: 0.6167 (m-80) cc_final: 0.5680 (m-80) outliers start: 24 outliers final: 21 residues processed: 100 average time/residue: 0.1754 time to fit residues: 25.9014 Evaluate side-chains 101 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.189550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.158735 restraints weight = 9267.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.157276 restraints weight = 13998.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.157164 restraints weight = 15459.334| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8696 Z= 0.223 Angle : 0.573 9.032 11975 Z= 0.295 Chirality : 0.043 0.259 1306 Planarity : 0.004 0.062 1388 Dihedral : 15.754 74.276 1369 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.25 % Allowed : 17.35 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.27), residues: 931 helix: 1.02 (0.30), residues: 332 sheet: -0.94 (0.39), residues: 149 loop : -1.01 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 383 HIS 0.003 0.001 HIS A 315 PHE 0.012 0.001 PHE B 130 TYR 0.011 0.001 TYR B 319 ARG 0.002 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 376 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8169 (m) REVERT: A 500 GLN cc_start: 0.7520 (mp10) cc_final: 0.7204 (mt0) REVERT: B 346 PHE cc_start: 0.6175 (m-80) cc_final: 0.5717 (m-80) outliers start: 27 outliers final: 23 residues processed: 101 average time/residue: 0.1746 time to fit residues: 26.1181 Evaluate side-chains 103 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 60 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.191042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.161013 restraints weight = 9160.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.158813 restraints weight = 15221.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.159792 restraints weight = 14815.534| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8696 Z= 0.189 Angle : 0.562 8.508 11975 Z= 0.289 Chirality : 0.042 0.251 1306 Planarity : 0.004 0.062 1388 Dihedral : 15.580 73.264 1369 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.65 % Allowed : 18.31 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.27), residues: 931 helix: 1.05 (0.30), residues: 334 sheet: -0.82 (0.40), residues: 149 loop : -0.96 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 383 HIS 0.003 0.001 HIS B 208 PHE 0.010 0.001 PHE B 130 TYR 0.009 0.001 TYR B 144 ARG 0.002 0.000 ARG A 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6317 (pm20) REVERT: A 376 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8091 (m) REVERT: A 500 GLN cc_start: 0.7578 (mp10) cc_final: 0.7253 (mt0) REVERT: B 346 PHE cc_start: 0.6040 (m-80) cc_final: 0.5606 (m-80) outliers start: 22 outliers final: 16 residues processed: 103 average time/residue: 0.1715 time to fit residues: 26.2158 Evaluate side-chains 102 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.186934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.156113 restraints weight = 9309.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.154194 restraints weight = 15137.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.154923 restraints weight = 14112.513| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8696 Z= 0.323 Angle : 0.628 8.950 11975 Z= 0.322 Chirality : 0.045 0.251 1306 Planarity : 0.004 0.065 1388 Dihedral : 15.739 74.445 1369 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.65 % Allowed : 18.67 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.27), residues: 931 helix: 0.86 (0.29), residues: 330 sheet: -0.97 (0.40), residues: 149 loop : -1.02 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 383 HIS 0.004 0.001 HIS A 315 PHE 0.029 0.002 PHE B 87 TYR 0.012 0.002 TYR A 181 ARG 0.004 0.000 ARG A 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2270.20 seconds wall clock time: 40 minutes 41.62 seconds (2441.62 seconds total)